Table 2.

Tests for linkage disequilibrium based on the standardised index of association, which approaches zero in recombining populations.

Phylogroup	Non-clone-corrected					Clone-corrected
	Genomes	No. called SNPs1	LD corrected SNPs2	% SNPs removed under LD	rbarD3	Genomes	No. called SNPs1	LD corrected SNPs2	% SNPs removed under LD	rbarD3
1	256	1 630 980	714 955	56	0.014	61	802 433	413 923	48	0.002
2	13	197 928	140 357	29	0.111	9	183 604	136 284	26	0.057
3	8	150 897	102 449	32	0.155	4	120 558	95 211	21	0.018
4	3	99 029	93 548	6	0.245	NA	NA	NA	NA	NA
5	61	625 191	352 735	44	0.025	28	401 258	238 426	41	0.008
6	23	70 319	54 140	23	0.455	9	63 419	54 160	15	0.316
7	7	141 561	120 891	15	0.228	4	136 590	119 677	12	0.004
8	5	117 541	100 285	15	0.326	4	114 316	99 302	13	0.220
9	27	471 669	310 211	34	0.026	17	440 908	296 782	33	0.021
10	1	NA	NA	NA	NA	NA	NA	NA	NA	NA
11	1	NA	NA	NA	NA	NA	NA	NA	NA	NA
12	5	144 481	124 829	14	0.337	3	132 108	119 599	9	0.021
All	410	4 664 221	4 628 213	1	0.0344	136	748 225	377 645	50	0.0384

¹Number of SNPs from a k-mer search (k = 31 for phylogroups, k = 101 for all) of coding sequences within each phylogroup using kSNP.

²SNPs were filtered based on an r² cutoff of 0.9999 calculated in PLINK.

³Calculated from bitwise.ia across LD corrected SNPs in poppr.

⁴Calculated from samp.ia with 1 000 repeats of 1 000 SNPs in poppr.